Current macroscopic arrays rely on large quantities of material extracted by PCR from target cells using fluorescent primers to label the target DNA. We have recently disclosed a method for making nanoscale arrays from self-assembly of DNA in such a way as to expose single stranded probes. (WO2006/124089 published Nov. 23, 2006, incorporated by reference herein in its entirety) The present invention provides improvements allowing these and other nucleic acid tiling arrays to be used directly inside the contents of single cells or with very small volumes of sample.